Nemesis definitely would have the advantage in some categories of Death Battle. Heavy arsenal, more mobility, and given his final boss nature, definitely the damage sponge. Big Daddy has the scary drill arm and maybe plasmids, and he is also a damage sponge, albeit a weaker one.
Hmm, The Daddy is definitely the more likeable combatant. But The Nemesis is a %$@ing badass. I think a big factor would be if Nemesis only gets to use his rocket launcher and not the minigun they gave him in the movie. I wouldn't count the movie though and not just because they're know for being bad, but because I'd prefer to stick to the game's cannon. Personally I'd want to the Daddy to win, but Nemesis is a force to be reckoned with.